Re: [R] install packages question

From: Peter Dalgaard <p.dalgaard_at_biostat.ku.dk>
Date: Tue 03 Oct 2006 - 07:35:21 GMT

"Leeds, Mark (IED)" <Mark.Leeds@morganstanley.com> writes:

> I am at a new job where my sys admin installed R in linux and it does
> run when I log in as a user. I am on linux 2.1.2 but i'm not sure if
> it''s redhat etc ( but i doubt this matters for my question ).

Well it does, since your sysadmin seems to need help. If it is Redhat/SuSE/Debian/Ubuntu/..., then he will have much easier installation options. "cat /etc/issue" should give you a clue what you're running. ("2.1.2" doesn't ring any bells with me, and neither does the use of kshell)

> The alias put in my .envfile ( for the kshell ) is
>
> R =
> "/ms/dev/fsf/R/2.0.0/install/.exec/ia32.linux.2.4.lib6/lib/R/bin/exec/R"

This is wrong. R need to be started via its startup script. "..../lib/R/bin/R" might be right.   

> and my R_HOME is
> /ms/dev/fsf/R/2.0.0/install/.exec/ia32.linux.2.4.lib6/lib/R

This should not be set at all.

Notice also that R-2.0.0 is two years old. It really shouldn't be necessary for you to run something that aged, and it can easily get you into trouble with packages developed against newer versions.

> So now, I am trying to install specific packages ( I can't use
> install.packages because my linux doesn't have an internet connection )
> , I think I found the right documentation
> ( pg 16 of R installation and administration ) and I set my R_LIBS
> varaible appropriately but my R CMD INSTALL command is not working. It
> just drops the CMD and gives "ARGUMENT CMD __ignored__ ) and invokes R
> by itself. I also tried R CMD BATCH testfile and similarly it dropped
> the CMD and the BATCH and just invoked R also

These are all symptoms of the above misconfiguration.   

> Does anyone know what I need to change ( probably in my .envfile ) so
> that R knows what these commands mean ? I am familar with installing R
> ( binary ) and various packages
> on windows but I am very unfamilar with Linux.
>
> I think if I can get this fixed, I might be able to install the specific
> packages I need because the instructions on pg 16 are clear. Thanks a
> lot.

You might need to get development tools installed (compilers, library stubs) if you have compiled code.

-- 
   O__  ---- Peter Dalgaard             ุster Farimagsgade 5, Entr.B
  c/ /'_ --- Dept. of Biostatistics     PO Box 2099, 1014 Cph. K
 (*) \(*) -- University of Copenhagen   Denmark          Ph:  (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)                  FAX: (+45) 35327907

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Received on Tue Oct 03 17:44:46 2006

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